Alkylating agents represent a broad group of environmental compounds, chemotherapeutic medicines and endogenous molecules that damage DNA bases via SN1 or SN2 reactions. Cellular proteins involved in DNA repair, DNA recombination and cell cycle arrest are important for maintaining viability and genomic integrity after challenge by the alkylating agent, methyl methanesulfonate (MMS). Nucelosomal proteins that manipulate DNA architecture have also been proposed to contribute to the detoxification of this alkylating agent. Indeed, our pilot data has identified some nucleosomal proteins as being important for alkylation resistance. The hypothesis that genes involved in nucleosome architecture play an important role in maintaining cellular viability after MMS exposure will be tested in this proposal. First, a set of over 4800 individual yeast gene deletion strains will be used in high throughput assays to identify genes required to maintain viability after MMS exposure. Over 100,000 data points will be generated from this study and they will be organized into an Internet accessible public database to allow for a further analysis of results by others and us. Secondly, computational analysis of our results will incorporate yeast protein interaction data to identify protein complexes, whose corresponding gene deletion strains show sensitivity to MMS. This will identify protein complexes important for defending the cell against damage by MMS and along with data clustering methods help identify other important pathways and cellular strategies required to combat the effects of macromolecular alkylation. Thirdly, we will explore the role that proteins involved in nucleosome structure have on modulating DNA alkylation damage. This will be done using assays that analyze cellular responses to MMS and assays that measure DNA damage levels after MMS exposure. Collectively, these studies will help us identify important cellular pathways activated in response to alkylating agents and the resultant database will be useful to elucidate the mechanism of action of MMS and identify strategies that increase the potency of clinically relevant alkylating agents.